<<

TABLE S1. Data characterized for this study.

rDNA 3

- -

Culture 3 - etK sp70cyt rc5 f1a f2 ps22a ps23a Lineage accession # Lab sec61 SSU 14 40S Atub Btub E E G H M R R T SUM Heteromita globosa 50780 Katz 1 1 Cercomonadida Bodomorpha minima 50339 Katz 1 1 Capsellina sp. 50039 Katz 1 1 1 1 4 Gymnophrea Gymnophrys sp. 50923 Katz 1 1 2 Cercomonadida marina 50266 Katz 1 1 1 1 4 sp. T7 Katz 1 1 2 Foraminifera Ovammina opaca Katz 1 1 1 1 4 Gromia sp. Katz 1 1 Proleptomonas Proleptomonas faecicola 50735 Katz 1 1 1 1 4 Theratromyxa Theratromyxa weberi 50200 Katz 1 1 50519 Katz 1 1 Fornicata Trepomonas agilis 50286 Katz 1 1 Soginia “Soginia anisocystis” 50646 Katz 1 1 1 1 1 5 Stephanopogon apogon 50096 Katz 1 1 Carolina hemisphaerica 13-1310 Katz 1 1 2 Cercomonadida Heteromita sp. PRA-74 MBL 1 1 1 1 1 1 1 7 Corallomyxa tenera 50975 MBL 1 1 1 3 papillatum 50162 MBL 1 1 1 1 1 1 1 1 8 Euglenozoa saltans CCAP1907 MBL 1 1 1 1 1 5 50194 MBL 1 1 1 1 4 sp. 50593 MBL 1 1 2

Katz lab work based on genomic PCRs and MBL (Marine Biological Laboratory) data are all from EST analyses. Culture accession number is ATTC unless noted. GenBank accession numbers for new sequences (including paralogs) are GQ377645-GQ377715 and HM244866-HM244878.

TABLE S2. Lineages based on Patterson 1999 with updates from Adl et al., 2005. Lineages Lineages Clade Genes Amoebozoa 15 Nucleariidae Opisthokonta 5 Rhizaria 1 Opisthokonta 16 Allantion Rhizaria 1 Oxymonadida 5 Allas Rhizaria 1 Excavata 16 Alveolates Alveolates 16 Paradinium Rhizaria 1 * - 5 Paramonas 1 Apusomonads - 6 Paramyxea - 1 - 12 Amoebozoa 2 Centroheliozoa - 7 Rhizaria 1 Cercomonadida Rhizaria 10 Amoebozoa 2 Chlamydomyxa Stramenopiles 1 Plamsmodiophorida Rhizaria 4 Rhizaria 14 Pleurostomum Excavata 1 - 1 Polycystinea Rhizaria 2 Cryothecomonas Rhizaria 1 Proleptomonas Rhizaria 4 Cryptomonads 10 Red 14 Desmothoracids Rhizaria 2 Soginia Excavata 5 Dimorphid Rhizaria 4 Stephanopogon Excavata 5 Ebriid Rhizaria 1 Rhizaria 1 Ellobiopsids Alveolates 1 Stramenopiles Stramenopiles 16 Amoebozoa 16 - 4 Euglenozoa Excavata 16 Thaumatomonads Rhizaria 4 Euglyphida Rhizaria 4 Theratromyxa Rhizaria 1 Eumycetozoa Amoebozoa 16 Trichosphaerium Amoebozoa 4 Flabellinea Amoebozoa 2 Excavata 16 Foraminifera Rhizaria 10 Tubulinea Amoebozoa 14 Diplomonadida Excavata 16 Vampryellidae Rhizaria 1 Excavata 5 Viridaeplantae Viridaeplantae 16 Glaucophytes 16 Xenophyophores Rhizaria 1 Gromia Rhizaria 3 Actinophryids Stramenopiles Gymnophrea Rhizaria 5 Biomyxa - Haplosporidia Rhizaria 2 Caecitellus Stramenopiles Haptophytes 15 Coelosporidium - Heterolobosea Excavata 16 Copromyxids - Hyperamoeba Amoebozoa 4 Discocelis Stramenopiles Excavata 14 - Kathablepharids Cryptomonads 7 Gymnosphaerida - Leukarachnion Stramenopiles 4 - Excavata 15 Luffisphaera - Mastigamoebidae Amoebozoa 16 Nephridiophagids Opisthokonta Mesomycetozoa Opisthokonta 15 Phagodinium - Metopion Rhizaria 1 Pseudodendromonads Stramenopiles Metromonas Rhizaria 1 Pseudospora - Ministeria Opisthokonta 8 Excavata Amoebozoa 1 Spironemidae - These eukaryotic lineages, defined by ultrastructural identities (Patterson, 1999), have proven robust in analyses with multiple datatypes (Parfrey et al. 2006; Simpson and Patterson 2006; Yoon et al. 2008). The lone exception is ‘ramicristates’, which is now divided between Amoebozoa and Rhizaria. Thus, lineages within Amoebozoa and Euglyphida are based on the classification of Adl et al. 2005. Clade = Higher-level grouping into which lineage has been subsummed (e.g. (Pawlowski and Burki 2009; Simpson and Patterson 2006)). Genes = number of genes in this study. *The identity of this taxon was recently clarified and Planomonas is a junior synonym (Heiss et al. 2010). See Table S4 for more detail on genes included in analysis. TABLE S3. -coding genes used in this study Homolo name Alternate gene names Gene IDs Taxa

Grf4 (General regulatory factor4) tyrosine 3-monooxygenase/tryptophan 14-3-3 5-monooxygenase activation protein 100743 87 40S 40S ribosomal protein S4 90857 82 Actin actin, beta 110648 197 Atub tubulin, alpha 4a 68496 158 Btub tubulin, beta 4 55952 161 eukaryotic elongation factor 1 Ef1α alpha 1 105313 98 EF2 eukaryotic translation elongation factor 2 100816 86 Enolase enolase 1 68183 84 Grc5 60S ribosomal protein L10 68830 87 Hsp70cyt heat shock 70kDa protein 8 68524 94 Hsp90 90kDa alpha (cytosolic) 74306 130 methionine adenosyltransferase II alpha, MetK S-adenosylmethionine synthetase 38112 77 Rps22a Rps15a (ribosomal protein S15A) 111120 77 ribosomal protein S23 Rps23a 40S ribosomal protein S23 799 86 Tsec61 Sec61 alpha 1 subunit 55537 77

Gene: The protein-coding genes included in this study, with the abbreviation corresponding to the data matrix. Alternate gene names are taken from HomoloGene. HomoloGene IDs are from www.ncbi.nlm.nih.gov/HomoloGene/. Taxa: number of taxa with protein-coding gene sequences in our analysis. TABLE S4. Details on individual genes by taxa

Lineage based on

Patterson 1999,

Supergroup Taxon

rDNA 3

- updated with Adl et. -

3 al., 2005 -

SSU 14 40S Actin Atub Btub Ef1a Ef2 Enolase Grc5 Hsp70cyt Hsp90 MetK Rps22a Rps23a Tsec61 Sum Amoebozoa Entamoebidae histolytica 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 Amoebozoa Eumycetozoa discoideum 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 Phreatamoeba balamuthi Amoebozoa Mastigamoebidae () 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 ‘’ Glaucophytes Cyanophora paradoxa 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 ‘Archaeplastida’ Viridaeplantae Arabidopsis thaliana 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 ‘Archaeplastida’ Viridaeplantae Ginkgo biloba 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 ‘Archaeplastida’ Viridaeplantae Oryza sativa 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 ‘Archaeplastida’ Viridaeplantae Physcomitrella patens 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 ‘’ Alveolates parvum 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 ‘Chromalveolata’ Alveolates tetraurelia 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 ‘Chromalveolata’ Alveolates berghei 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 ‘Chromalveolata’ Alveolates thermophila 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 ‘Chromalveolata’ Alveolates 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 ‘Chromalveolata’ Alveolates parva 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 ‘Chromalveolata’ Stramenopiles Phaeodactylum tricornutum 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 ‘Chromalveolata’ Stramenopiles 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 Excavata Euglenozoa major 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 Excavata Euglenozoa brucei 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 Excavata Diplomonadida lamblia ATCC 50803 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 Excavata Heterolobosea gruberi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 Excavata Jakobids Seculamonas ecuadoriensis' 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 Excavata Parabasalids vaginalis 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 Trimastix pyriformis ATCC Excavata Trimastix 50562 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 Opisthokonta Opisthokonta Caenorhabditis elegans 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 Opisthokonta Opisthokonta Candida albicans 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 Opisthokonta Opisthokonta Ciona intestinalis 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 Opisthokonta Opisthokonta Drosophila melanogaster 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 Opisthokonta Opisthokonta Gallus gallus 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 Opisthokonta Opisthokonta Homo sapiens 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 Opisthokonta Opisthokonta Saccharomyces cerevisiae 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 Opisthokonta Opisthokonta Schizosaccharomyces pombe 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 Opisthokonta Opisthokonta Nematostella vectensis 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 Amoebozoa Acanthamoebidae castellanii 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 15 Amoebozoa Eumycetozoa polycephalum 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 15 ‘Archaeplastida’ Viridaeplantae Chlamydomonas reinhardtii 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 15 ‘Archaeplastida’ Viridaeplantae Micromonas pusilla 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 15 ‘Archaeplastida’ Viridaeplantae carteri 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 15 ‘Chromalveolata’ Alveolates marinus 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 15 ‘Chromalveolata’ Haptophytes 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 15 ‘Chromalveolata’ Haptophytes galbana 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 15 ‘Chromalveolata’ Stramenopiles Aureococcus anophagefferens 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 15 ‘Chromalveolata’ Stramenopiles infestans 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 15 Excavata Jakobids americana 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 15 Excavata Malawimonas Malawimonas jakobiformis 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 15 Opisthokonta Opisthokonta Branchiostoma floridae 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 15 Opisthokonta Opisthokonta Monosiga brevicollis 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 15

Lineage based on

Patterson 1999,

rDNA 3

Supergroup Taxon

- -

updated with Adl et. 3 al., 2005 -

SSU 14 40S Actin Atub Btub Ef1a Ef2 Enolase Grc5 Hsp70cyt Hsp90 MetK Rps22a Rps23a Tsec61 Sum Opisthokonta Opisthokonta Phanerochaete chrysosporium 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 15 Opisthokonta Opisthokonta Strongylocentrotus purpuratus 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 15 Opisthokonta Opisthokonta Ustilago maydis 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 15 Opisthokonta Mesomycetozoa owczarzaki 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 15 Amoebozoa Tubulinea vermiformis 1 1 1 1 1 1 1 1 1 1 1 1 1 1 14 ‘Archaeplastida’ Red algae Porphyra yezoensis 1 1 1 1 1 1 1 1 1 1 1 1 1 1 14 ‘Archaeplastida’ Viridaeplantae Mesostigma viride 1 1 1 1 1 1 1 1 1 1 1 1 1 1 14 ‘Archaeplastida’ Viridaeplantae Welwitschia mirabilis 1 1 1 1 1 1 1 1 1 1 1 1 1 1 14 ‘Chromalveolata’ Alveolates 1 1 1 1 1 1 1 1 1 1 1 1 1 1 14 Excavata Euglenozoa gracilis 1 1 1 1 1 1 1 1 1 1 1 1 1 1 14 Excavata Euglenozoa Diplonema papillatum 1 1 1 1 1 1 1 1 1 1 1 1 1 1 14 Excavata Euglenozoa Euglena longa 1 1 1 1 1 1 1 1 1 1 1 1 1 1 14 Opisthokonta Opisthokonta Encephalitozoon cuniculi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 14 Opisthokonta Opisthokonta Schistosoma mansoni 1 1 1 1 1 1 1 1 1 1 1 1 1 1 14 Opisthokonta Mesomycetozoa 1 1 1 1 1 1 1 1 1 1 1 1 1 1 14 Rhizaria Chlorarachniophyta natans 1 1 1 1 1 1 1 1 1 1 1 1 1 1 14 ‘Archaeplastida’ Glaucophytes Glaucocystis nostochinearum 1 1 1 1 1 1 1 1 1 1 1 1 1 13 ‘Archaeplastida’ Red algae Chondrus crispus 1 1 1 1 1 1 1 1 1 1 1 1 1 13 ‘Chromalveolata’ Haptophytes Pavlova lutheri 1 1 1 1 1 1 1 1 1 1 1 1 1 13 ‘Chromalveolata’ Haptophytes parvum 1 1 1 1 1 1 1 1 1 1 1 1 1 13 ‘Chromalveolata’ Stramenopiles hominis 1 1 1 1 1 1 1 1 1 1 1 1 1 13 Excavata Diplomonadida vortens 1 1 1 1 1 1 1 1 1 1 1 1 1 13 Excavata Heterolobosea marylandensis 1 1 1 1 1 1 1 1 1 1 1 1 1 13 Excavata Oxymonadida strix 1 1 1 1 1 1 1 1 1 1 1 1 1 13 Allomyces macrogynus ATCC Opisthokonta Opisthokonta 38327 1 1 1 1 1 1 1 1 1 1 1 1 1 13 Opisthokonta Opisthokonta Aplysia californica 1 1 1 1 1 1 1 1 1 1 1 1 1 13 ‘Chromalveolata’ Alveolates Nyctotherus ovalis 1 1 1 1 1 1 1 1 1 1 1 1 12 Excavata Diplomonadida Spironucleus barkhanus 1 1 1 1 1 1 1 1 1 1 1 1 12 Excavata Jakobids libera 1 1 1 1 1 1 1 1 1 1 1 1 12 Opisthokonta Opisthokonta Mnemiopsis leidyi 1 1 1 1 1 1 1 1 1 1 1 1 12 Opisthokonta Opisthokonta Oscarella carmela 1 1 1 1 1 1 1 1 1 1 1 1 12 Opisthokonta Opisthokonta Spizellomyces punctatus 182 1 1 1 1 1 1 1 1 1 1 1 1 12 Other Breviata Breviata anathema 1 1 1 1 1 1 1 1 1 1 1 11 ‘Chromalveolata’ Alveolates Entodinium caudatum 1 1 1 1 1 1 1 1 1 1 1 11 ‘Chromalveolata’ Alveolates brevis 1 1 1 1 1 1 1 1 1 1 1 11 ‘Chromalveolata’ Cryptophyta theta 1 1 1 1 1 1 1 1 1 1 10 Opisthokonta Opisthokonta Capitella capitata 1 1 1 1 1 1 1 1 1 1 1 11 Opisthokonta Mesomycetozoa parasiticum 1 1 1 1 1 1 1 1 1 1 1 11 ‘Chromalveolata’ Alveolates tenella 1 1 1 1 1 1 1 1 1 1 10 ‘Chromalveolata’ Alveolates Chilodonella uncinata 1 1 1 1 1 1 1 1 1 1 10 Heteromita (chimera of H. globosa and H sp. ATCC PRA- Rhizaria Cercomonadida 74) 1 1 1 1 1 1 1 1 1 1 10 Rhizaria Foraminifera filosa 1 1 1 1 1 1 1 1 1 1 10 ‘Archaeplastida’ Acetabularia acetabulum 1 1 1 1 1 1 1 1 1 9 Opisthokonta Opisthokonta Glomus intraradices 1 1 1 1 1 1 1 1 1 9 Excavata Euglenozoa 1 1 1 1 1 1 1 1 8 Opisthokonta Ministeria Ministeria vibrans 1 1 1 1 1 1 1 1 8 ‘Archaeplastida’ Red algae Cyanidioschyzon merolae 1 1 1 1 1 1 1 7

Lineage based on

Patterson 1999,

rDNA 3

Supergroup Taxon

- -

updated with Adl et. 3 al., 2005 -

SSU 14 40S Actin Atub Btub Ef1a Ef2 Enolase Grc5 Hsp70cyt Hsp90 MetK Rps22a Rps23a Tsec61 Sum ‘Chromalveolata’ Stramenopiles Apodachlya brachynema 1 1 1 1 1 1 1 7 ‘Chromalveolata’ Stramenopiles 1 1 1 1 1 1 1 7 Excavata Jakobids incarcerata 1 1 1 1 1 1 1 7 Excavata Jakobids Andalucia godoyi 1 1 1 1 1 1 1 7 Other Kathablepharids marina 1 1 1 1 1 1 1 7 Rhizaria Corallomyxa tenera 1 1 1 1 1 1 1 7 Amoebozoa incertae sedis Arachnula sp. ATCC 50593 1 1 1 1 1 1 6 ‘Chromalveolata’ Alveolates neurona 1 1 1 1 1 1 6 ‘Chromalveolata’ Alveolates rotundata 1 1 1 1 1 1 6 ‘Chromalveolata’ Alveolates marina 1 1 1 1 1 1 6 ‘Chromalveolata’ Alveolates Gregarina niphandrodes 1 1 1 1 1 1 6 ‘Chromalveolata’ Cryptophyta truncata 1 1 1 1 1 1 6 Excavata Diplomonadida inflata 1 1 1 1 1 1 6 Monocercomonas sp. ATCC Excavata Parabasalids 50210 1 1 1 1 1 1 6 Opisthokonta Opisthokonta amphoridium 1 1 1 1 1 1 6 Opisthokonta Mesomycetozoa limacisporum 1 1 1 1 1 1 6 proboscidea Other Apusomonads CCAP 1905/1 1 1 1 1 1 1 6 Other Centroheliozoa contractilis 1 1 1 1 1 1 6 ‘Chromalveolata’ Alveolates 1 1 1 1 1 5 ‘Chromalveolata’ Alveolates lemnae 1 1 1 1 1 5 ‘Chromalveolata’ Stramenopiles Mallomonas rasilis 1 1 1 1 1 5 ‘Chromalveolata’ Stramenopiles Phytophthora palmivora 1 1 1 1 1 5 Excavata Carpediemonas Carpediemonas membranifera 1 1 1 1 1 5 sp. Excavata Oxymonadida PA203 1 1 1 1 1 5 Excavata Parabasalids agilis 1 1 1 1 1 5 ATCC 50646 (“Soginia Excavata Soginia anisocystis”) 1 1 1 1 1 5 Excavata Stephanopogon Stephanopogon apogon 1 1 1 1 1 5 simplex CCAP Opisthokonta Nucleariidae 1552/4 1 1 1 1 1 5 Opisthokonta Opisthokonta Rhizopus microsporus 1 1 1 1 1 5 Opisthokonta Opisthokonta Diaphanoeca grandis 1 1 1 1 1 5 Opisthokonta Opisthokonta Aphrocallistes vastus 1 1 1 1 1 5 Ancyromonas micra ATCC Other Ancyromonas 50267 1 1 1 1 1 5 Rhizaria Cercomonadida Massisteria marina 1 1 1 1 1 5 Rhizaria Gymnophrea Gymnophrys sp. ATCC 50923 1 1 1 1 1 5 Hyperamoeba sp. ATCC PRA- Amoebozoa Hyperamoeba 39 1 1 1 1 4 Amoebozoa incertae sedis Parvamoeba monoura 1 1 1 1 4 Trichosphaerium sp. ATCC Amoebozoa Trichosphaerium 40318 1 1 1 1 4 Amoebozoa Tubulinea Nolandella sp. ATCC PRA-27 1 1 1 1 4 Amoebozoa Tubulinea sp. ATCC 50933 1 1 1 1 4 ‘Archaeplastida’ Green algae Coleochaete scutata 1 1 1 1 4 ‘Archaeplastida’ Green algae Chlorella vulgaris 1 1 1 1 4 ‘Chromalveolata’ Alveolates Prorocentrum minimum 1 1 1 1 4

Lineage based on

Patterson 1999,

rDNA 3

Supergroup Taxon

- -

updated with Adl et. 3 al., 2005 -

SSU 14 40S Actin Atub Btub Ef1a Ef2 Enolase Grc5 Hsp70cyt Hsp90 MetK Rps22a Rps23a Tsec61 Sum ‘Chromalveolata’ Alveolates foliaceum 1 1 1 1 4 ‘Chromalveolata’ Alveolates japonicum 1 1 1 1 4 ‘Chromalveolata’ Alveolates 1 1 1 1 4 ‘Chromalveolata’ Cryptophyta sp. CCMP1868 1 1 1 1 4 ‘Chromalveolata’ Cryptophyta mesostigmatica 1 1 1 1 4 ‘Chromalveolata’ Haptophytes polylepis 1 1 1 1 4 ‘Chromalveolata’ Leukarachnion Leukarachnion sp. 1 1 1 1 4 ‘Chromalveolata’ Stramenopiles Pelagomonas calceolata 1 1 1 1 4 ‘Chromalveolata’ Stramenopiles Thraustochytrium striatum 1 1 1 1 4 Excavata Euglenozoa Entosiphon sulcatum 1 1 1 1 4 Excavata Euglenozoa sp. ATCC 50226 1 1 1 1 4 Excavata Heterolobosea 1 1 1 1 4 Excavata Heterolobosea cosmopolitus 1 1 1 1 4 Excavata Parabasalids Holomastigotoides mirabile 1 1 1 1 4 Excavata Trimastix Trimastix marina 1 1 1 1 4 other Telonema Telonema antarcticum 1 1 1 1 4 other Telonema Telonema subtile 1 1 1 1 4 Cercomonas sp. ATCC PRA- Rhizaria Cercomonadida 21 1 1 1 1 4 Rhizaria Cercomonadida Bodomorpha minima 1 1 1 1 4 Rhizaria Dimorphid Dimorpha sp. ATCC PRA-54 1 1 1 1 4 Rhizaria Euglyphida Capsellina sp 1 1 1 1 4 Rhizaria Foraminifera Ovammina opaca 1 1 1 1 4 Rhizaria Plamsmodiophorida brassicae 1 1 1 1 4 Rhizaria Proleptomonas Proleptomonas faecicola 1 1 1 1 4 Rhizaria Thaumatomonads Thaumatomonas seravini 1 1 1 1 4 Amoebozoa Eumycetozoa violaceum 1 1 1 3 Amoebozoa Tubulinea 1 1 1 3 Amoebozoa Tubulinea proteus 1 1 1 3 ‘Chromalveolata’ Alveolates striatus 1 1 1 3 ‘Chromalveolata’ Alveolates palaeformis 1 1 1 3 ‘Chromalveolata’ Alveolates willei 1 1 1 3 ‘Chromalveolata’ Alveolates octocarinatus 1 1 1 3 ‘Chromalveolata’ Alveolates Monocystis agilis 1 1 1 3 ‘Chromalveolata’ Alveolates sp. AP309 1 1 1 3 ‘Chromalveolata’ Stramenopiles Nitzschia thermalis 1 1 1 3 ‘Chromalveolata’ Stramenopiles sp. N12 1 1 1 3 Excavata Euglenozoa helicis 1 1 1 3 Excavata Euglenozoa Rhynchobodo sp. ATCC 50359 1 1 1 3 Excavata Diplomonadida Enteromonas hominis 1 1 1 3 Excavata Diplomonadida Trimitus sp. TRION 1 1 1 3 Excavata Oxymonadida exilis 1 1 1 3 Excavata Oxymonadida grandis 1 1 1 3 Opisthokonta Opisthokonta Trachipleistophora hominis 1 1 1 3 Opisthokonta Opisthokonta Stephanoeca diplocostata 1 1 1 3 Rhizaria Chlorarachniophyta Gymnochlora stellata 1 1 1 3 Rhizaria Foraminifera sp. 1 1 1 3 Rhizaria Foraminifera Rhabdammina cornuta 1 1 1 3

Lineage based on

Patterson 1999,

rDNA 3

Supergroup Taxon

- -

updated with Adl et. 3 al., 2005 -

SSU 14 40S Actin Atub Btub Ef1a Ef2 Enolase Grc5 Hsp70cyt Hsp90 MetK Rps22a Rps23a Tsec61 Sum Gromia (chimera of G. Rhizaria Gromia oviformis G. sp Antarctica) 1 1 1 3 Rhizaria incertae sedis Spongomonas ATCC 50405 1 1 1 3 Amoebozoa Eumycetozoa denudata 1 1 2 Amoebozoa Eumycetozoa flavogenita 1 1 2 Amoebozoa Eumycetozoa persimilis 1 1 2 Amoebozoa Flabellinea perurans 1 1 2 Amoebozoa Flabellinea Pessonella sp. PRA-29 1 1 2 Amoebozoa Flabellinea placida 1 1 2 Amoebozoa Flabellinea Dermamoeba algensis 1 1 2 Amoebozoa Flabellinea sp. JJP-2003 1 1 2 Amoebozoa Pelomyxa Pelomyxa palustris 1 1 2 Amoebozoa Phalansterium Phalansterium solitarium 1 1 2 Amoebozoa Thecamoebida similis 1 1 2 Amoebozoa Thecamoebida pedata 1 1 2 Amoebozoa Tubulinea carolinense 1 1 2 Amoebozoa Tubulinea mira 1 1 2 Amoebozoa Tubulinea Hartmannella cantabrigiensis 1 1 2 Amoebozoa Tubulinea sphagni 1 1 2 Amoebozoa Tubulinea hoguae 1 1 2 ‘Archaeplastida’ Red algae Glaucosphaera vacuolata 1 1 2 ‘Archaeplastida’ Red algae Nemalionopsis shawii 1 1 2 ‘Archaeplastida’ Red algae Rhodosorus marinus 1 1 2 ‘Archaeplastida’ Red algae Stylonema alsidii 1 1 2 ‘Chromalveolata’ Alveolates sp. 1 1 2 ‘Chromalveolata’ Cryptophyta Teleaulax acuta 1 1 2 ‘Chromalveolata’ Haptophytes 1 1 2 ‘Chromalveolata’ Stramenopiles Costaria costata 1 1 2 ‘Chromalveolata’ Stramenopiles Fucus disticus 1 1 2 ‘Chromalveolata’ Stramenopiles japonica 1 1 2 Excavata Euglenozoa cantuscygni 1 1 2 Excavata Diplomonadida Trepomonas agilis 1 1 2 Excavata Oxymonadida Saccinobaculus ambloaxostylus 1 1 2 Opisthokonta incertae sedis Micronuclearia podoventralis 1 1 2 Opisthokonta Opisthokonta Oreochromis esculentus 1 1 2 Opisthokonta Opisthokonta choanojuncta 1 1 2 Batrachochytrium Opisthokonta Opisthokonta dendrobatidis 1 1 2 Opisthokonta Opisthokonta Boothiomyces macroporosum 1 1 2 Other Centroheliozoa Chlamydaster sterni 1 1 2 other Kathablepharids remigera 1 1 2 Rhizaria Chlorarachniophyta Lotharella globosa 1 1 2 Rhizaria Desmothoracids Clathrulina elegans 1 1 2 Rhizaria Desmothoracids Hedriocystis reticulata 1 1 2 Rhizaria Euglyphida rotunda 1 1 2 Rhizaria Foraminifera Ammonia sp. T7 1 1 2 Rhizaria Foraminifera Amphisorus hemprichii 1 1 2 Rhizaria Foraminifera Globobulimina turgida 1 1 2 Rhizaria Foraminifera Astrammina rara 1 1 2

Lineage based on

Patterson 1999,

rDNA 3

Supergroup Taxon

- -

updated with Adl et. 3 al., 2005 -

SSU 14 40S Actin Atub Btub Ef1a Ef2 Enolase Grc5 Hsp70cyt Hsp90 MetK Rps22a Rps23a Tsec61 Sum Rhizaria Haplosporidia Bonamia ostreae 1 1 2 Rhizaria Haplosporidia Haplosporidium costale 1 1 2 Rhizaria Haplosporidia Haplosporidium louisiana 1 1 2 Rhizaria Haplosporidia 1 1 2 Rhizaria Haplosporidia Minchinia chitonis 1 1 2 Rhizaria Haplosporidia Urosporidium_crescens 1 1 2 Rhizaria incertae sedis Lecythium sp. 1 1 2 Rhizaria Plamsmodiophorida Sorosphaera_veronicae 1 1 2 Spongospora subterranea f. sp. Rhizaria Plamsmodiophorida subterranea 1 1 2 Rhizaria Polycystinea Collozoum inerme 1 1 2 Rhizaria Polycystinea Thalassicolla pellucida 1 1 2 Amoebozoa Acanthamoebidae 1 1 Amoebozoa Acanthamoebidae Comandonia operculata 1 1 Amoebozoa Acanthamoebidae Protacanthamoeba bohemica 1 1 Amoebozoa Entamoebidae nana 1 1 Amoebozoa Eumycetozoa dubium 1 1 Amoebozoa Eumycetozoa Didymium iridis 1 1 Amoebozoa Eumycetozoa Didymium nigripes 1 1 Amoebozoa Eumycetozoa carestianum 1 1 Amoebozoa Eumycetozoa Protophysarum phloiogenum 1 1 Pseudodidymium Amoebozoa Eumycetozoa cryptomastigophorum 1 1 Amoebozoa Eumycetozoa impexus 1 1 Amoebozoa Flabellinea sp. ATCC 50884 1 1 Amoebozoa Flabellinea stella 1 1 Amoebozoa Flabellinea leei 1 1 Amoebozoa Flabellinea Platyamoeba plurinucleolus 1 1 Amoebozoa Flabellinea aberdonica 1 1 Amoebozoa Flabellinea Vannella miroides 1 1 Amoebozoa Flabellinea armata 1 1 Amoebozoa Flabellinea Vexillifera minutissima 1 1 Amoebozoa Flabellinea spiniferum 1 1 Amoebozoa Flabellinea Platyamoeba stenopodia 1 1 Amoebozoa incertae sedis Filamoeba nolandi 1 1 sp. ATCC Amoebozoa incertae sedis 50654 1 1 Amoebozoa Mastigamoebidae Mastigamoeba simplex 1 1 Mastigamoeba sp. ATCC Amoebozoa Mastigamoebidae 50617 1 1 Amoebozoa Mastigamoebidae commutans 1 1 Amoebozoa Multicilia Multicilia marina 1 1 Amoebozoa Tubulinea Amoeba leningradensis 1 1 Amoebozoa Tubulinea laevigata 1 1 Amoebozoa Tubulinea Chaos nobile 1 1 Amoebozoa Tubulinea Echinamoeba exundans 1 1 Amoebozoa Tubulinea 1 1 Amoebozoa Tubulinea Paraflabellula reniformis 1 1 Amoebozoa Tubulinea Rhizamoeba saxonica 1 1 Amoebozoa Tubulinea Ripidomyxa sp. RP010 1 1

Lineage based on

Patterson 1999,

rDNA 3

Supergroup Taxon

- -

updated with Adl et. 3 al., 2005 -

SSU 14 40S Actin Atub Btub Ef1a Ef2 Enolase Grc5 Hsp70cyt Hsp90 MetK Rps22a Rps23a Tsec61 Sum Amoebozoa Tubulinea Saccamoeba limax 1 1 ‘Archaeplastida’ Glaucophytes Cyanoptyche gloeocystis 1 1 ‘Archaeplastida’ Red algae Bangiopsis subsimplex 1 1 ‘Archaeplastida’ Red algae Pterocladiella nana 1 1 ‘Archaeplastida’ Green algae Araucaria heterophylla 1 1 ‘Archaeplastida’ Green algae atmophyticus 1 1 ‘Archaeplastida’ Green algae Closterium ehrenbergii 1 1 ‘Archaeplastida’ Green algae Cycas taitungensis 1 1 ‘Archaeplastida’ Green algae Elliptochloris sp. E20-d 1 1 ‘Archaeplastida’ Green algae Geminella minor 1 1 ‘Archaeplastida’ Green algae Halimeda macrophysa 1 1 ‘Archaeplastida’ Green algae Kirchneriella aperta 1 1 ‘Archaeplastida’ Green algae Koliella planctonica 1 1 ‘Archaeplastida’ Green algae Lunularia cruciata 1 1 ‘Archaeplastida’ Green algae Lycopodium tristachyum 1 1 ‘Archaeplastida’ Green algae Oltmannsiellopsis geminata 1 1 ‘Archaeplastida’ Green algae Raphidonema nivale 1 1 ‘Archaeplastida’ Green algae Tetraselmis kochiensis 1 1 ‘Archaeplastida’ Green algae Zygnema cylindricum 1 1 ‘Chromalveolata’ Alveolates Adelina dimidiata 1 1 ‘Chromalveolata’ Alveolates octopiana 1 1 Amoebophrya sp. ex ‘Chromalveolata’ Alveolates Scrippsiella 1 1 ‘Chromalveolata’ Alveolates 1 1 ‘Chromalveolata’ Alveolates Bursaria truncatella 1 1 ‘Chromalveolata’ Alveolates 1 1 ‘Chromalveolata’ Alveolates sp. ATCC 50594 1 1 ‘Chromalveolata’ Alveolates Colpodidium caudatum 1 1 ‘Chromalveolata’ Alveolates acuminata 1 1 ‘Chromalveolata’ Alveolates fossata 1 1 ‘Chromalveolata’ Alveolates Gloeodinium viscum 1 1 ‘Chromalveolata’ Alveolates Hemidinium nasutum 1 1 ‘Chromalveolata’ Alveolates Ichthyodinium chabelardi 1 1 ‘Chromalveolata’ Alveolates Ophriocystis elektroscirrha 1 1 ‘Chromalveolata’ Alveolates Prorodon viridis 1 1 ‘Chromalveolata’ Alveolates Pyrocystis noctiluca 1 1 ‘Chromalveolata’ Alveolates Rhytidocystis polygordiae 1 1 Thoracosphaera heimii CCCM ‘Chromalveolata’ Alveolates 670 1 1 ‘Chromalveolata’ Alveolates pontica 1 1 Chlamydomyxa ‘Chromalveolata’ Chlamydomyxa labyrinthuloides 1 1 ‘Chromalveolata’ Cryptophyta paramecium 1 1 ‘Chromalveolata’ Cryptophyta Chilomonas sp. M1303 1 1 ‘Chromalveolata’ Cryptophyta rufescens 1 1 ‘Chromalveolata’ Ellobiopsids Thalassomyces fagei 1 1 ‘Chromalveolata’ Haptophytes Calcidiscus leptoporus 1 1 ‘Chromalveolata’ Haptophytes Corcontochrysis noctivaga 1 1 ‘Chromalveolata’ Haptophytes pouchetii 1 1 ‘Chromalveolata’ Paramonas Paramonas globosa 1 1

Lineage based on

Patterson 1999,

rDNA 3

Supergroup Taxon

- -

updated with Adl et. 3 al., 2005 -

SSU 14 40S Actin Atub Btub Ef1a Ef2 Enolase Grc5 Hsp70cyt Hsp90 MetK Rps22a Rps23a Tsec61 Sum ‘Chromalveolata’ Stramenopiles Blastocystis sp. H11 1 1 ‘Chromalveolata’ Stramenopiles Bolidomonas pacifica 1 1 ‘Chromalveolata’ Stramenopiles roenbergensis 1 1 ‘Chromalveolata’ Stramenopiles Chrysocapsa paludosa 1 1 ‘Chromalveolata’ Stramenopiles Ciliophrys infusionum 1 1 ‘Chromalveolata’ Stramenopiles Heterococcus pleurococcoides 1 1 ‘Chromalveolata’ Stramenopiles catenoides 1 1 ‘Chromalveolata’ Stramenopiles maritima 1 1 ‘Chromalveolata’ Stramenopiles Ochromonas danica 1 1 ‘Chromalveolata’ Stramenopiles Phaeomonas parva 1 1 ‘Chromalveolata’ Stramenopiles Phaeothamnion confervicola 1 1 ‘Chromalveolata’ Stramenopiles Picophagus flagellatus 1 1 ‘Chromalveolata’ Stramenopiles Pinguiochrysis pyriformis 1 1 ‘Chromalveolata’ Stramenopiles Schizocladia ischiensis 1 1 ‘Chromalveolata’ Stramenopiles Spumella elongata 1 1 ‘Chromalveolata’ Stramenopiles Wobblia lunata 1 1 Excavata Euglenozoa Astasia curvata 1 1 Excavata Euglenozoa culicis 1 1 pigra CCAP Excavata Euglenozoa 1212/1 1 1 Excavata Euglenozoa Distigma gracile 1 1 Excavata Euglenozoa Eutreptia viridis 1 1 Excavata Euglenozoa Gyropaigne lefevrei 1 1 Excavata Euglenozoa Herpetomonas roitmani 1 1 Excavata Euglenozoa spirogyroides 1 1 Excavata Euglenozoa brevicula 1 1 Excavata Diplomonadida intestinalis 1 1 Excavata incertae sedis Dysnectes brevis 1 1 Excavata Heterolobosea Heteramoeba clara 1 1 Excavata Heterolobosea Monopylocystis visvesvarai 1 1 Excavata Heterolobosea ustiana 1 1 Excavata Heterolobosea lanterna 1 1 Excavata Heterolobosea thermacidophilus 1 1 Excavata Heterolobosea avara 1 1 Excavata Heterolobosea Vahlkampfia damariscottae 1 1 Excavata Oxymonadida sp. NcOxA 1 1 Excavata Parabasalids Calonympha grassii 1 1 Excavata Parabasalids Deltotrichonympha operculata 1 1 Excavata Parabasalids 1 1 Excavata Parabasalids Hoplonympha sp. MO-2004-1 1 1 Excavata Parabasalids Joenia sp. KfJeA 1 1 Excavata Parabasalids Koruga bonita 1 1 Excavata Parabasalids Pentatrichomonoides scroa 1 1 Excavata Parabasalids Pseudotrypanosoma giganteum 1 1 Spirotrichonymphella sp. MO- Excavata Parabasalids 2004-1 1 1 Excavata Parabasalids Staurojoenina assimilis 1 1 Excavata Parabasalids Stephanonympha nelumbium 1 1 Excavata Parabasalids Teranympha mirabilis 1 1

Lineage based on

Patterson 1999,

rDNA 3

Supergroup Taxon

- -

updated with Adl et. 3 al., 2005 -

SSU 14 40S Actin Atub Btub Ef1a Ef2 Enolase Grc5 Hsp70cyt Hsp90 MetK Rps22a Rps23a Tsec61 Sum Excavata Pleurostomum Pleurostomum flabellatum 1 1 Excavata Stephanopogon Stephanopogon minuta 1 1 Opisthokonta Opisthokonta Sycon calcaravis 1 1 Opisthokonta Opisthokonta Monoblepharis macrandra 1 1 Opisthokonta Mesomycetozoa Amphibiothecum penneri 1 1 Opisthokonta Mesomycetozoa percae 1 1 Opisthokonta Opisthokonta Eccrinidus flexilis 1 1 Opisthokonta Opisthokonta Palavascia patagonica 1 1 Opisthokonta Opisthokonta Taeniella carcini 1 1 Other Apusomonads Amastigomonas debruynei 1 1 Other Apusomonads Amastigomonas mutabilis 1 1 Other Centroheliozoa Acanthocystis nichollsi 1 1 Other Centroheliozoa Choanocystis rotundata 1 1 Other Centroheliozoa Heterophrys marina 1 1 Other Centroheliozoa Polyplacocystis symmetrica 1 1 Other Centroheliozoa Pterocystis foliacea 1 1 Other Centroheliozoa Raineriophrys erinaceoides 1 1 Other Centroheliozoa Sphaerastrum fockii 1 1 Other Collodictyonidae 1 1 other Kathablepharids 1 1 Other Paramyxea Marteilioides chungmuensis 1 1 Rhizaria Acantharea Acanthometra sp. 1 1 Rhizaria Acantharea Amphiacon denticulatus 1 1 Rhizaria Acantharea Amphibelone anomala 1 1 Rhizaria Acantharea Arthracanthid 206 1 1 Rhizaria Acantharea Chaunacanthid 217 1 1 Rhizaria Acantharea Hexaconus serratus 1 1 Rhizaria Acantharea Symphyacanthid 211 1 1 Rhizaria Allantion Allantion sp. ATCC 50734 1 1 Rhizaria Allas Allas diplophysa 1 1 Rhizaria Cercomonadida Cercomonas agilis 1 1 Rhizaria Cercomonadida Neocercomonas jutlandica 1 1 Rhizaria Chlorarachniophyta Chlorarachnion reptans 1 1 Rhizaria Cryothecomonas Cryothecomonas longipes 1 1 Rhizaria Ebriid Ebria tripartita 1 1 Rhizaria Euglyphida Assulina seminulum 1 1 Rhizaria Euglyphida Corythion dubium 1 1 Rhizaria Euglyphida ampulla 1 1 Rhizaria Euglyphida Pseudodifflugia cf. gracilis 1 1 Rhizaria Euglyphida lineare 1 1 Rhizaria Foraminifera Borelis schlumbergeri 1 1 Rhizaria Foraminifera Cribrothalammina alba 1 1 Rhizaria Foraminifera Eggerelloides scabrum 1 1 Rhizaria Foraminifera Trochammina hadai 1 1 Rhizaria Gymnophrea Gymnophrys cometa 1 1 Rhizaria Haplosporidia Mikrocytos mackini 1 1 Rhizaria incertae sedis Aurigamonas solis 1 1 Rhizaria Metopion Metopion fluens 1 1 Rhizaria Metromonas Metromonas simplex 1 1

Lineage based on

Patterson 1999,

rDNA 3

Supergroup Taxon

- -

updated with Adl et. 3 al., 2005 -

SSU 14 40S Actin Atub Btub Ef1a Ef2 Enolase Grc5 Hsp70cyt Hsp90 MetK Rps22a Rps23a Tsec61 Sum Rhizaria incertae sedis Filoreta marina 1 1 Rhizaria Paradinium Paradinium poucheti 1 1 Rhizaria Paradinium Paradinium sp. PaEu41 1 1 Rhizaria Phaeodarea Aulacantha scolymantha 1 1 Rhizaria Phaeodarea trigonopa 1 1 Rhizaria Phaeodarea Challengeron diodon 1 1 Rhizaria Phaeodarea Coelodendrum_ramosissimum 1 1 Rhizaria Phaeodarea Conchellium capsula 1 1 Rhizaria Phaeodarea Protocystis xiphodon 1 1 Rhizaria Plamsmodiophorida Maullinia ectocarpii 1 1 Rhizaria Plamsmodiophorida Phagomyxa odontellae 1 1 Rhizaria Plamsmodiophorida Polymyxa betae 1 1 Rhizaria Polycystinea Acrosphaera sp. CR6A 1 1 Rhizaria Polycystinea Artostrobus sp. 2014 1 1 Rhizaria Polycystinea Didymocyrtis tetrathalamus 1 1 Rhizaria Polycystinea Eucyrtidium hexastichum 1 1 Rhizaria Polycystinea Larcopyle butschlii 1 1 Rhizaria Polycystinea Lithomelissa sp. 8012 1 1 Rhizaria Polycystinea Pseudocubus obeliscus 1 1 Rhizaria Polycystinea Pterocanium trilobum 1 1 Rhizaria Polycystinea Pterocorys zancleus 1 1 Rhizaria Polycystinea cyathina 1 1 Rhizaria Polycystinea Sphaerozoum punctatum 1 1 Rhizaria Polycystinea Spongaster tetras 1 1 Rhizaria Polycystinea Stylodictya sp. 8037 1 1 Rhizaria Polycystinea Styptosphaera sp. 2022 1 1 Rhizaria Polycystinea Tetrapyle octacantha 1 1 Rhizaria Sticholonche Sticholonche sp. JJP-2003 1 1 Rhizaria Thaumatomonads Protaspis grandis 1 1 Thaumatomastix sp. ATCC Rhizaria Thaumatomonads 50250 1 1 Rhizaria Theratromyxa Theratromyxa weberi 1 1 sp. Fritzlar- Rhizaria Vampryellid Werkel 1 1 Rhizaria Xenophyophores sp. BBL-2008 1 1

TABLE S5. Support for major from additional analyses comparing taxon and gene sets from other studies

Supported clades Hampl: 16 gene Yoon: 16 gene All: 4 gene

Opisthokonta 100 93 98 Rhizaria 100 100 89 SAR 95 100 nm Rhizaria + stramenopiles 80 93 nm Excavata 82 nm nm Amoebozoa 99 44 44 ‘Unikonta' 99 nm nm

Weak/unsupported hypotheses

‘Archaeplastida’ 32 nm nm ‘Chromalveloata' nm nm nm Cryptomonads + haptophytes na nm 16 Haptophytes + SAR 73 58 nm Alveolates + stramenopiles nm nm 25 Red algae + green algae 64 nm nm Red, Green, Glauco, Hapto, Crypt na nm nm

Dataset statistics Number of taxa 48 101 168 Number of lineages 19 26 46 % Missing data (characters) 21 39 11

Additional analyses with taxon selection based on recent published analyses to explore tradeoffs between taxon and gene sampling (see methods and Table 1 for more details). ‘Hampl: 16 gene’ and ‘Yoon: 16 gene’ includes all 16 genes with taxon selection based on Hampl et al. 2009 and

Yoon et al. 2008. ‘All: 4 gene’ is an analysis of four commonly sampled markers (actin, alpha tubulin, beta tubulin, and ssu-rDNA) and all of our taxa with at least 3 of these 4 genes. See

Figure S1j-l for individual trees. TABLE S6. Support for major clades from additional analyses that attempt to address EGT.

EGT EGT - -

Supported clades 5: non 3: non 3: caterp 7 gene 5: caterp 13 gene 5: caterp 9 gene 10:16 no HC

Opisthokonta 94 89 17 96 96 100 Rhizaria 100 81 29 98 nm 100 SAR nm 55 20 78 nm 100 Rhizaria + stramenopiles nm 28 18 67 nm 79 Excavata nm 27 02 56 nm 84 Amoebozoa nm nm 11 95 51 66 ‘Unikonta' nm nm 05 92 nm 57

Weak/unsupported hypotheses

‘Archaeplastida’ nm nm nm nm nm nm ‘Chromalveloata' nm nm nm nm nm na Cryptomonads + haptophytes nm nm nm nm nm na Haptophytes + SAR nm 57 17 73 31 na Alveolates + stramenopiles nm nm nm nm nm na Red algae + green algae nm nm nm nm nm 81 Red, Green, Glauco, Hapto, Crypt nm nm nm nm nm nm

Dataset statistics Number of taxa 77 91 91 90 111 83 Number of lineages 23 26 25 25 30 24 % Missing data (characters) 8 11 16 17 19 20

Additional analyses to further explore the impact of subsampling genes and taxa to account for EGT on clade support (see methods and Table 1 for more details). ‘5: non-EGT’ and ‘3: non- EGT’ include taxa with at least 5 of 7 (or 3 of 7) candidate genes not likely to have originated by EGT in BLAST analysis. ‘3: caterp 7 gene’ includes taxa with at least 3 of 7 genes identified as largest concordant gene set by Concaterpillar, plus ssu-rDNA. ‘5: caterp 13 gene’ includes taxa with at least 5 of 13 genes; three excluded genes were not concordant with any others according to Concaterpillar. ‘5: caterp 9 gene’ includes taxa with at least 5 of 9 genes; gene sampling is largest concordant gene set identified by Concaterpillar run on only photosynthetic taxa. ‘10:16 no HC’ is the 10:16 dataset with haptophytes and cryptomonads removed. See Figure S1m-r for individual trees. Na= not able to evaluate. TABLE S7. Topology tests of ‘Archaeplastida’, ‘Chromalveolata’ and ‘’ hypotheses

Topology au kh sh wkh wsh np pp mb Most likely 0.811 0.781 0.924 0.781 0.927 0.779 0.780 1 ‘Archaeplastida’ monophyletic 0.226 0.219 0.359 0.219 0.324 0.216 0.216 <0.001 0 ‘Chromalveolata’ monophyletic 0.007 0.005 0.019 0.005 0.009 0.004 0.004 <0.001 0 ‘Chromista’ monophyletic <0.001 <0.001 <0.001 <0.001 <0.001 <0.001 <0.001 <0.001 0

Topology on 10:16 dataset to assess alternative hypotheses. Topology tests p-values for approximately unbiased test (au), Kishino–Hasegawa test (kh) , Shimodaira–Hasegawa test (sh), weighted Kishino–Hasegawa test (skh) , weighted Shimodaira–Hasegawa test (wsh) . Non- parametric bootstrap probability (np) calculated from multiscale bootstrap, bootstrap probability (bp) calculated in the non-multiscale manner, Bayesian posterior probability (pp) calculated by Bayesian information-criterion approximation. The number of trees consistent with the given hypotheses (mb) in the 10,756 output trees of Bayesian analysis after stationarity. Results in bold significantly reject monophyly. All analyses except mb from Consel (Shimodaira and Hasegawa, 2001). TABLE S8. Position of unplaced ‘orphan’ lineages

Taxon Sistergroup Analysis BS taxon sistergroup analysis BS Ancyromonas Opisthokonta 4: 16 54 Centroheliozoa Haptophytes 6: 16 29 Ancyromonas Micronuclearia all: 16 27 Centroheliozoa Red algae 4: 16 26 Ancyromonas in Rhizaria 3: 15 3 Centroheliozoa Entamoebidae all: 16 5 Ancyromonas Micronuclearia all: 15 20 Centroheliozoa Breviata 5: 15 9 Ancyromonas Breviata all: 4 gene 26 Centroheliozoa Breviata 3: 15 7 Apusomonads Opisthokonta 6: 16 98 Centroheliozoa Breviata all: 15 11 Apusomonads Opisthokonta 4: 16 89 Centroheliozoa Red algae all: 4 gene 79 Apusomonads Opisthokonta all: 16 12 Centroheliozoa Red algae 5: caterp 9 39 Apusomonads Opisthokonta 5: 15 99 Diphylleia Entamoebidae all: 16 2 Apusomonads Opisthokonta 3: 15 65 Kathablepharids Cryptomonads 6: 16 85 Apusomonads Opisthokonta all: 15 9 Kathablepharids Cryptomonads 4: 16 57 Apusomonads Opisthokonta all: 4 gene 99 Kathablepharids Cryptomonads all: 16 56 Apusomonads Opisthokonta 5: caterp 9 96 Kathablepharids Cryptomonads 5: 15 66 Breviata Opisthokonta 10: 16 17 Kathablepharids Haptophytes 3: 15 27 Breviata Centroheliozoa 6: 16 8 Kathablepharids Haptophytes all: 15 32 Breviata Amoebozoa 4: 16 8 Kathablepharids Cryptomonads all: 4 gene 66 Breviata Entamobidae all: 16 2 Kathablepharids Cryptomonads 5: caterp 9 86 Breviata Opisthokonta 9: 15 21 Micronuclearia Ancyromonas all: 16 27 Breviata Centroheliozoa 5: 15 9 Micronuclearia Ancyromonas all: 15 20 Breviata Centroheliozoa 3: 15 7 Mikrocytos in Euglenozoa all: 16 34 Breviata Centroheliozoa all: 15 11 Paramyxea Trichosphaerium all: 16 72 Breviata Ancyromonas all: 4 gene 26 Telonema Green algae 4: 16 25 Breviata Andalucia 5: caterp 9 3 Telonema Green algae all: 16 24 Breviata Opisthokonta 3: EGT 18 Telonema Green algae 3: 15 27 Breviata Malawimonas 3: caterp 7 29 Telonema Green algae all: 15 25 Telonema Stramenopiles all: 4 gene 32

We examined the position of unplaced lineages across our analyses. Our analysis reveals strongly supported sistergroup relationships for two previously unplaced lineages, apusomonads and kathablepharids. The sistergroup relationship of apusomonads + Opisthokonta is strongly supported across analyses. The relationship between kathablepharids and cryptomonads is recovered in all but one analysis; in all:15 cryptomonads are sister to the kathablepharid+ clade. In addition, Telonema consistently branches with green algae but with low support. The remaining lineages have yet to find stable homes, as evidenced by varying sistergroups and low support. BS: Bootstrap values calculated from analyses described in Tables 1 and S6.

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